Reconstructing diploid 3D chromatin structures from single cell Hi-C data with a polymer-based approach
Loading...
Date issued
Editors
Journal Title
Journal ISSN
Volume Title
Publisher
Reuse License
Abstract
Detailed understanding of the 3D structure of chromatin is a key ingredient to investigate a variety of processes inside the cell. Since direct methods to experimentally ascertain these structures lack the desired spatial fidelity, computational inference methods based on single cell Hi-C data have gained significant interest. Here, we develop a progressive simulation protocol to iteratively improve the resolution of predicted interphase structures by maximum-likelihood association of ambiguous Hi-C contacts using lower-resolution predictions. Compared to state-of-the-art methods, our procedure is not limited to haploid cell data and allows us to reach a resolution of up to 5,000 base pairs per bead. High resolution chromatin models grant access to a multitude of structural phenomena. Exemplarily, we verify the formation of chromosome territories and holes near aggregated chromocenters as well as the inversion of the CpG content for rod photoreceptor cells.
Description
Keywords
Citation
Published in
Frontiers in bioinformatics, 3, Frontiers, Lausanne, 2023, https://doi.org/10.3389/fbinf.2023.1284484